Calcium in PDB 3bdj: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor

All present enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor:
1.17.1.4; 1.17.3.2;

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor, PDB code: 3bdj was solved by B.T.Eger, K.Okamoto, T.Nishino, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.517, 124.074, 148.797, 90.00, 91.01, 90.00
R / Rfree (%)	19.1 / 22.4

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	8 atoms

The binding sites of Calcium atom in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor (pdb code 3bdj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor, PDB code: 3bdj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5301 b:15.1 occ:1.00 OG A:SER907 2.6 12.6 1.0 O A:ALA867 2.6 12.5 1.0 O A:SER870 2.6 16.7 1.0 OG A:SER874 2.7 13.8 1.0 O A:ASN908 2.8 15.1 1.0 O A:ARG871 3.0 17.4 1.0 C A:ARG871 3.5 16.2 1.0 N A:ASN908 3.5 13.5 1.0 C A:ALA867 3.7 14.0 1.0 C A:SER870 3.7 16.4 1.0 CB A:ASP872 3.8 16.1 1.0 CB A:SER907 3.8 12.5 1.0 C A:ASN908 3.8 14.6 1.0 CB A:SER874 3.9 14.7 1.0 C A:SER907 4.0 14.3 1.0 CA A:SER907 4.0 12.8 1.0 CB A:ALA867 4.0 12.2 1.0 NE2 A:HIS840 4.1 16.7 1.0 CA A:ARG871 4.1 16.4 1.0 CA A:ALA867 4.2 14.0 1.0 N A:ASP872 4.2 15.5 1.0 CA A:ASN908 4.2 14.4 1.0 N A:ARG871 4.3 16.7 1.0 OG A:SER870 4.4 18.2 1.0 CA A:ASP872 4.5 15.4 1.0 N A:SER874 4.6 13.9 1.0 CE1 A:HIS840 4.7 15.5 1.0 N A:SER870 4.8 17.4 1.0 CA A:SER870 4.8 17.2 1.0 N A:GLY868 4.8 13.2 1.0 CA A:SER874 4.8 15.9 1.0 O A:SER907 4.8 14.9 1.0 CB A:ASN908 4.9 13.8 1.0 N A:LEU873 4.9 13.4 1.0 CG A:ASP872 4.9 15.1 1.0 C A:ASP872 5.0 15.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5302 b:15.4 occ:1.00 O B:ALA867 2.5 16.1 1.0 OG B:SER907 2.6 15.6 1.0 OG B:SER874 2.7 15.2 1.0 O B:SER870 2.7 17.1 1.0 O B:ASN908 2.8 14.9 1.0 O B:ARG871 3.0 16.5 1.0 N B:ASN908 3.6 16.8 1.0 C B:ALA867 3.6 16.9 1.0 C B:ARG871 3.6 17.2 1.0 C B:SER870 3.7 17.2 1.0 CB B:ASP872 3.8 14.1 1.0 C B:ASN908 3.8 17.1 1.0 CB B:SER907 3.8 15.2 1.0 CB B:SER874 3.9 16.4 1.0 CB B:ALA867 4.0 15.8 1.0 C B:SER907 4.0 17.8 1.0 CA B:ALA867 4.1 16.9 1.0 NE2 B:HIS840 4.1 17.6 1.0 CA B:SER907 4.1 15.5 1.0 CA B:ARG871 4.2 18.4 1.0 CA B:ASN908 4.3 16.4 1.0 N B:ASP872 4.3 16.6 1.0 OG B:SER870 4.4 17.3 1.0 N B:ARG871 4.4 17.9 1.0 N B:SER874 4.6 15.5 1.0 CA B:ASP872 4.6 15.5 1.0 CE1 B:HIS840 4.6 15.2 1.0 N B:GLY868 4.7 17.2 1.0 N B:SER870 4.7 15.5 1.0 CA B:SER870 4.8 17.3 1.0 CA B:SER874 4.8 16.4 1.0 CB B:ASN908 4.8 18.2 1.0 O B:SER907 4.9 17.3 1.0 CG B:ASP872 4.9 17.0 1.0 N B:LEU873 5.0 13.8 1.0 CA B:GLY868 5.0 18.3 1.0

K.Okamoto, B.T.Eger, T.Nishino, E.F.Pai, T.Nishino. Mechanism of Inhibition of Xanthine Oxidoreductase By Allopurinol: Crystal Structure of Reduced Bovine Milk Xanthine Oxidoreductase Bound with Oxipurinol. Nucleosides Nucleotides V. 27 888 2008NUCLEIC Acids.
ISSN: ISSN 1525-7770
PubMed: 18600558
DOI: 10.1080/15257770802146577